United States 

Department of 

Agriculture 

Animal and Plant 

Health Inspection 

Service 

 

APHIS 91–45–016 

Uniform Program 

Standards for the 

Voluntary Bovine 

Johne’s Disease 

Control Program 

Effective September 1, 

2010
 2

The U.S. Department of Agriculture (USDA) prohibits discrimination in all its 

programs and activities on the basis of race, color, national origin, sex, religion, 

age, disability, political beliefs, sexual orientation, or marital or family status. 

(Not all prohibited bases apply to all programs.) Persons with disabilities who 

require alternative means for communication of program information (Braille, 

large print, audiotape, etc.) should contact USDA’s TARGET Center at (202) 

720–2600 (voice and TDD). To file a complaint of discrimination, write USDA, 

Director, Office of Civil Rights, Room 326–W, Whitten Building, 1400 

Independence Avenue, SW., Washington, DC 20250–9410, or call (202) 720–

5964 (voice and TDD). USDA is an equal opportunity provider and employer. 

Issued September 2010 
 3

Contents 

Introduction 

I. Definitions and Abbreviations 

II. Administration of the Program 

A. Designated Johne’s Disease Coordinator 

B. State JD Group 

C. Johne’s Disease Certified Veterinarians 

D. Premises Biosecurity 

E. Exceptions to Deadlines 

F. Administrative Review of a State’s VBJDCP Activities and 

Progress 

III. Program Elements and Procedures 

A. Education 

B. Management Level 

C. Herd Testing and Classification 

IV. Laboratory Procedures 

A. Approved Laboratories 

B. Laboratory Approval Process 

C. Approved Program Tests 

Appendix 1: Sampling Sizes and Random Selection for Statistical Subset Testing 

Appendix 2: Approved Testing Strategies for the Classification Component 

Appendix 3: Johne’s Disease Certified Veterinarian Training Guidelines 

Appendix 4: Appealing the Status of a Test-positive Animal 
 4

Introduction 

Title 9, Code of Federal Regulations (9 CFR), part 71, contains general 

provisions for the interstate transportation of animals, poultry, and animal 

products, while part 80 pertains specifically to the interstate movement of 

domestic animals that are positive to an official test for Johne’s disease (JD). 

These regulations provide that cattle, sheep, goats, and other domestic animals 

that are positive to an official test for JD may generally be moved interstate only 

to a recognized slaughtering establishment or to an approved livestock facility for 

sale to such an establishment. The animals must bear an official eartag and be 

shipped with an owner-shipper statement. 

Supplementing the regulations is the Uniform Program Standards for the 

Voluntary Bovine Johne’s Disease Control Program (VBJDCP) that outlines the 

national standards of the program and provides specific information on 

administration of the program, program elements and procedures, and laboratory 

procedures. This document describes the cooperative VBJDCP to be administered 

by the State and supported by industry and the Federal Government. This 

publication is intended as a working document that will change as the program 

develops. 

The objective of this program is to provide national standards for the control of 

JD. The program consists of three basic elements: 1) education to inform 

producers about the cost of JD and to provide information about management 

strategies to prevent, control, and eliminate the disease; 2) management to work 

with producers to establish good management strategies on their farms; and 3) 

herd testing and classification to demonstrate the level of risk of JD on the farm. 

The program has been developed in cooperation with the National Johne’s 

Disease Working Group and the Johne’s disease committee of the United States 

Animal Health Association, State Veterinarians, and industry representatives. The 

program has been approved by the USDA’s Animal and Plant Health Inspection 

Service (APHIS), Veterinary Services (VS). 

The national standards described in this document do not preclude the adoption of 

more stringent methods and rules by any geographical or political subdivision of 

the United States with regard to activities within its boundaries; however, 

regulations dealing with interstate movement must conform to Federal 

regulations. 
 5

I. Definitions and Abbreviations 

Accredited veterinarian 

A veterinarian approved by the APHIS Administrator in accordance with the 

provisions of 9 CFR, part 161, to perform functions required by State-FederalIndustry cooperative programs. 

 

Administrator 

The Administrator of APHIS or any person authorized to act for the 

Administrator. 

Animal and Plant Health Inspection Service (APHIS) 

The Animal and Plant Health Inspection Service of the United States Department 

of Agriculture. 

Animal health official 

An employee of the State animal health department or of APHIS who has 

authority from the State Veterinarian or the Area Veterinarian in Charge to carry 

out program activities. 

Anniversary date 

The date on which the designated Johne’s disease coordinator gave final approval 

for initial program participation for a herd. 

 

Approved laboratory 

A private, State, Federal, or university laboratory that has passed the annual check 

test for JD administered by the National Veterinary Services Laboratories 

(NVSL). The Administrator approves a laboratory to conduct an official or 

screening JD test only after determining that the laboratory meets the check test 

proficiency requirements prescribed by NVSL. Approval continues as long as 

such check test proficiency requirements are met annually. All program testing 

must be done in a laboratory approved by NVSL for the specific test being used in 

a State’s testing program. 

Area Veterinarian in Charge (AVIC) 

An APHIS veterinarian authorized by the Administrator to supervise and manage 

the animal health work of APHIS in a specified area of the United States. 

Authorized agent 

A qualified individual authorized by the State animal health official to perform 

sample collections for the VBJDCP. This person shall have completed training 

specified by the designated JD coordinator for JD epidemiology. The State 

animal health official will also specify the types of samples that may be collected 

by the authorized agent. 

CFR 

Code of Federal Regulations
 6

Check test 

A panel of samples developed and released annually by NVSL to determine if 

participating laboratories are proficient at detecting positive samples (antibody or 

organism detection) within an expected range of accuracy. 

Classification 

Categorization of a herd based upon the results and years of Johne’s disease 

testing performed on eligible animals within the herd. 

Clinical disease in cattle 

Generally characterized by one or more of the following clinical signs: severe 

weight loss, profuse diarrhea, edema, or a significant drop in milk production. 

Commingling 

Animals grouped together having direct contact with the same facilities, 

equipment, individuals, or environment under circumstances where unprotected 

contact may spread disease. For example, all cattle in the same pen, corral, or 

vehicle or all cattle grazed together on the same area of a property or farm will be 

considered commingled. 

Designated JD coordinator (DJC) 

An individual who has demonstrated the knowledge and ability to perform the 

functions required under these program standards and who has been selected for 

this position by the State animal health official and the AVIC. The VS regional 

JD epidemiologist and the VS JD headquarters’ staff must concur in the selection 

and appointment of the DJC. 

ELISA 

Enzyme-linked immunosorbent assay. 

Exposure 

Contact with known infected animals, contact with the manure or raw milk of 

infected or exposed animals of susceptible species, or contact with infected herds 

via contaminated water or feed sources including runoff from neighboring 

premises. 

Herd 

A group of animals managed as a separate and discrete unit. This may include two 

or more geographically separated groups of animals under common ownership or 

supervision but have an interchange or movement of animals without regard to 

health status. The DJC will make the final determination of the herd status of a 

group of animals. 

Herd Classification Test 

The testing of a statistically appropriate group or subset of test-eligible animals 

from a herd. Depending on the herd size this may include all test-eligible animals. 
 7

(See Appendix 1: Sampling Sizes and Random Selection for Statistical Subset

Testing.) 

Herd management plan 

See management plan below. 

Herd member 

An animal of any susceptible species that is commingled with the herd. 

Infected animal 

An animal that has been found by an official JD test to be infected with 

Mycobacterium avium subsp. Paratuberculosis. 

Infected herd 

A herd that has one or more individual animals, pooled fecal samples or 

environmental samples found positive on an official JD test. 

Johne’s disease (JD) 

An infectious, communicable, and incurable disease, also known as 

paratuberculosis, that primarily affects cattle, sheep, goats, and other domestic, 

exotic, and wild ruminants and is caused by Mycobacterium avium subsp.

paratuberculosis (MAP). 

Johne’s disease Certified Veterinarian (JCV) 

An accredited veterinarian who has completed training approved by the DJC for 

JD epidemiology and development of herd management plans. 

Johne’s disease test 

Diagnostic test used to aid in determining if an animal has been exposed to or is 

infected with Mycobacterium avium subspecies paratuberculosis. Test 

terminology used by the VBJDCP: 

 Environmental fecal sampling 

A manure sample that is collected from areas where fecal material from 

which a large proportion of the herd is commingled. The sample is tested 

using a MAP detection test. 

 Official Johne’s disease test (OJT) 

An individual organism detection test approved by the Administrator and 

conducted in a laboratory approved by the Administrator. A list of 

currently approved laboratories and the requirements for obtaining 

approval are available from the Diagnostic Bacteriology Laboratory, 

NVSL, P.O. Box 844, Ames, IA 50010. A laboratory will be approved 

only after demonstrating that it meets the check test proficiency 

requirements prescribed by the NVSL on an annual basis. 
 8

 MAP detection test (MAPDT) 

An organism detection test approved by the Administrator and specific for 

MAP. This includes either screening (multiple animals or environmental) 

or official (individual) tests conducted in a laboratory approved by the 

Administrator. A list of currently approved laboratories and the 

requirements for obtaining approval are available from the Diagnostic 

Bacteriology Laboratory, NVSL, P.O. Box 844, Ames, IA 50010. A 

laboratory will be approved only after demonstrating that it meets the 

check test proficiency requirements prescribed by the NVSL on an annual 

basis. 

 Screening test 

A test approved by the Administrator for use in the VBJDCP and 

conducted in an approved laboratory to diagnose MAP to aid in 

determining the presence or absence of MAP within a herd. A screening 

test cannot be used to classify an individual animal for the purposes of the 

program. An animal found positive by a screening test should be 

considered a JD suspect and may be further tested using an official JD test. 

However, if the animal is showing clinical signs of JD or is from a herd 

previously diagnosed with MAP, it should be considered positive based on 

a screening test. 

Level achievement year 

The year a herd obtained its current classification in the herd testing and 

classification element of the program. 

Management herd 

A herd that is enrolled in the program and meets the management component 

requirements described in this document. 

Management plan 

A written plan produced by the JD certified veterinarian or animal health official 

in conjunction with the producer that includes animal husbandry and hygiene 

practices specific to that herd and is designed to limit opportunities for exposure 

to MAP. The plan is developed following the completion of a risk assessment for 

the operation. 

Mycobacterium avium subsp. paratuberculosis 

The causative agent of Johne’s disease, sometimes referred to as MAP or 

Mycobacterium paratuberculosis. 

NCAHP 

National Center for Animal Health Programs. 

National Johne’s Disease Coordinator 

The lead staff veterinarian responsible for the coordination of the National 

Johne’s Disease Control Program for Veterinary Services, National Center for 

Animal Health Programs. 
 9

National Veterinary Services Laboratories 

The APHIS laboratory that supports the Johne’s program is the Diagnostic 

Bacteriology Laboratory, USDA, APHIS, VS, NVSL 1800 Dayton Road, P.O. 

Box 844, Ames, IA 50010. The Internet site for this laboratory can be found at 

http://www.aphis.usda.gov/animal_health/lab_info_services/about_dbl.shtml. 

 

Official eartag 

An eartag that provides a unique, nontransferable identification for an individual 

animal. An official eartag must bear the U.S. shield. The design, size, shape, 

color, and other characteristics of the official eartag will depend on the needs of 

the users. The tag must be tamper-resistant and must have been shown to have a 

high retention rate in the animal. These tags must adhere to one of the following 

numbering systems: 

1. National Uniform Eartagging System. 

2. Animal identification number (AIN). 

3. Premises-based number system. The premises-based number system combines 

an official premises identification number (PIN), as defined in this section, 

with a producer’s livestock production numbering system to provide a unique 

identification number. The PIN and the production number must both appear 

on the official tag. 

4. Any other numbering system approved by the Administrator for the 

identification of animals in commerce. 

Premises identification number (PIN) 

A unique number assigned by a State or Federal animal health authority to a 

premises that is, in the judgment of the State or Federal animal health authority, a 

geographically distinct location from other livestock production units. The PIN is 

associated with an address or legal land description and may be used in 

conjunction with a producer’s own livestock production numbering system to 

provide a unique identification number for an animal. The PIN may consist of: 

1. The State’s two-letter postal abbreviation followed by the premises’ assigned 

number. 

2. A seven-character alphanumeric code, with the right-most character being a 

check digit. The check digit number is based upon the ISO 7064 Mod 36/37 

check digit algorithm. 

Program 

Voluntary Bovine Johne’s Disease Control Program (VBJDCP). 

RAMP 

The combination of the risk assessment (RA) and the development of a herd 

management plan (MP). This can be accomplished during separate visits or in a 

single visit of the Johne’s disease certified veterinarian or animal health official. 
 10

Risk assessment 

An evaluation of the facilities and management practices performed by a JCV or 

animal health official in conjunction with the producer that includes an evaluation 

of the animal husbandry and hygiene practices specific to that herd that may 

provide opportunities for exposure to MAP. The risk assessment is performed 

prior to developing a herd management plan and periodically afterward to assess 

the current risk status of the herd. 

State 

Any of the 50 States, the Commonwealth of Puerto Rico, the Commonwealth of 

the Northern Mariana Islands, the District of Columbia, and any Territories and 

possessions of the United States. 

State animal health official 

The State official responsible for livestock and poultry disease control and 

eradication programs. 

State JD Group 

A group of individuals organized by the State animal health official to assist in the 

oversight and coordination of the State’s Johne’s disease program. 

Susceptible species 

Domestic and exotic ruminants, such as cattle, bison, sheep, goats, cervids, and 

camelids that are capable of being infected through natural exposure with MAP.

Test-eligible animals 

Female bovine animals 36 months of age or greater and male bovine animals 

24 months of age or greater. 

USDA 

United States Department of Agriculture. 

VBJDCP 

Voluntary Bovine Johne’s Disease Control Program. 

Veterinary Services (VS) 

The division of APHIS in charge of Federal animal health activities within the 

United States. 
 11

II. Administration of the Program 

A. Designated Johne’s Disease Coordinator 

1. General 

Each State must designate at least one individual to act as its DJC. This 

person should be selected jointly by the State animal health official and 

the AVIC, and approved by the VS regional JD epidemiologist or 

Regional Director and the National Johne’s Disease Coordinator of VS’ 

NCAHP. 

2. Qualifications 

Each DJC candidate must: 

a. Be a State, Federal, or university-employed veterinarian 

b. Successfully complete a JD education course approved by the National 

Johne’s Disease Coordinator. Course instructions include on-farm Risk 

RAMP training 

c. Have at least 80 hours experience in assessing risk, developing herd 

plans, and classifying JD tested animals and herds 

d. Attend continuing education provided by APHIS when necessary 

After being selected and approved, a DJC may be given a 1-year grace 

period to allow the candidate to meet the education and training 

requirements 

3. Responsibilities 

The DJC has the responsibility to: 

a. Interpret laboratory test results and classify animals and herds based 

on the use of official and screening tests 

b. Provide training for personnel performing program work 

c. Provide training for JCV and develop a mechanism to evaluate and 

monitor the involvement of the JCV 

d. Review and approve the RAMPs for participating/program herds 

e. Periodically audit the program, and herds within the program, to 

determine if it is adequately achieving its goals and objectives 
 12

f. Assist JCV, animal health officials, and herd owners with the 

development of herd management plans as requested or needed 

g. Participate in the program activities as a member of the State JD group 

h. Provide required reports to the Area Office, VS regional JD 

epidemiologist, and the JD staff of VS’ NCAHP on the progress of the 

program 

B. State JD Group 

1. General 

The State JD group will assist the State in program development, 

implementation, and review. The group must meet at least once a year. 

2. Recommended members 

This group should include pertinent stakeholders, such as: 

a. Dairy producers—purebred, commercial, and/or commodity groups 

b. Beef producers—purebred, commercial, and/or commodity groups 

c. University and extension faculty 

d. Animal health diagnostic laboratory personnel 

e. Regulatory veterinary medical officers (State or Federal) 

f. Veterinary practitioners—beef and dairy 

It is recommended that a beef or dairy producer serve as the chairperson 

for the group. The DJC must be a member. 

C. Johne’s Disease Certified Veterinarians 

1. General 

States may elect to use the services of private practitioners in addition to 

State or Federal personnel to assist herd owners in conducting RAMPs. 

States using these veterinarians must determine that they meet the 

qualifications listed below. The DJC needs to develop a process to closely 

monitor the herd management plans developed by new JCVs. For 

example, the DJC may require the new JCV to develop the first one-tofive herd management plans in conjunction with an experienced animal 

health official. 
 13

2. Qualifications 

JCVs must be accredited veterinarians, must have received additional 

education on JD, and must be able to demonstrate to the DJC that they 

have the knowledge needed to: 

a. Perform appropriate JD risk assessments 

b. Develop approved herd management plans 

c. Understand JD epidemiology, testing, and test interpretation 

d. Understand State and Federal program requirements 

e. Collect and submit appropriate samples for JD testing 

3. Training 

In order to maintain consistent competency levels of JCVs between States, 

a curriculum has been outlined in Appendix 3: Johne’s Disease Certified 

Veterinarian Training Guidelines. At least once every 5 years, JCVs must 

complete a JD refresher course approved by the DJC and outlined in 

Appendix 3. 

4. Responsibilities 

JCVs have the responsibility to: 

a. Develop RAMPs at the request of herd owners that will meet the 

approval of the DJC 

b. Collect and submit samples according to the requirements set by the 

DJC 

D. Premises Biosecurity 

Individuals working on the VBJDCP must use sanitary procedures to 

minimize the risk of transmitting infectious diseases to other premises. 

E. Exceptions to Deadlines 

Animal health officials must follow deadlines for the herd management plan 

and testing except when a DJC determines that there are extenuating 

circumstances. The extenuating circumstances must make it impossible to 

meet the deadline established for a particular herd. The animal health official 

will set a new deadline in consultation with the herd owner, or his or her 

representative, to accomplish the required activities at the earliest opportunity. 
 14

The new deadline must be consistent with the principles of JD control and 

eradication. 

F. Administrative Review of a State’s VBJDCP Activities and Progress 

An administrative review of a State’s VBJDCP may involve any or all of the 

following: 

1. VS personnel will conduct ongoing reviews at local and national levels by 

receiving and examining routine monthly, quarterly, annual, and other 

statistical and narrative reports that have been prepared and submitted by 

the State or Federal animal health officials in each of the States. 

2. The National Johne’s Disease Coordinator will monitor the results of 

existing State policies and procedures for controlling and eradicating JD 

by examining factors such as the test/activity and herd management plans. 

3. The National Johne’s Disease Coordinator will evaluate the information 

provided by the various States in special reports regarding the authorities 

and policies for implementing the various minimum standards of the 

State’s VBJDCP. 

4. Regional Directors, a regional epidemiologist, and VS staff personnel will 

visit various States to observe program procedures and to make general or 

specific evaluations. 

5. Special evaluation teams comprised of several individuals representing 

State, Federal, industry, and academic interests will make visits to 

designated States to make limited or comprehensive reviews of the State’s 

VBJDCP. 
 15

III. Program Elements and Procedures 

A. Education 

1. General 

The education element in a State serves as the entry level for producers to 

participate in the State’s voluntary JD control program. This element 

should provide producers with basic JD information, effective 

management strategies for controlling and eliminating the disease, and 

information on the various aspects of the State’s program. Education can 

take place through group workshops, one-on-one sessions, or through 

online training. A record of participation should be kept. In the education 

element of the program, producers should receive information on the 

topics indicated below. 

2. Required topics for education 

a. Basic JD information: cause, clinical stages, transmission, etc. 

b. Management strategies for: 

1) Manure and waste 

2) Colostrum and milk 

3) Calves and young stock 

4) Additions and high-risk animals 

5) Biosecurity 

6) Infected animals 

c. Control and testing strategies, including: 

1) Testing options 

2) Test interpretation 

3) Using test results 

d. State program components 

1) Options for program participation 

 
 16

B. Management Level 

 

1. General 

 Producers informed about JD may wish to participate in the management 

level of the program, which recognizes producers for implementing 

meaningful management practices to control the introduction or spread of 

MAP. At this level, any individual animal or herd testing is optional but 

strongly encouraged. JD testing should be based on a plan with clear 

action determined prior to testing. JD testing protocols can be developed 

using the guidelines provided in the “Consensus recommendations on 

diagnostic testing for the detection of paratuberculosis in cattle in the 

United States” published in the December 12, 2006, Journal of American 

Veterinary Medical Association. Reporting test results is not required; 

while not required, testing should be done in an approved laboratory to 

ensure the validity of the test results. 

2. Requirements 

The following components must be completed to the satisfaction of the 

DJC: 

a. Risk assessment 

Before developing a herd management plan, a JCV must conduct a risk 

assessment to identify management practices and facility issues likely 

to introduce and spread MAP throughout the herd. A copy of the risk 

assessment must be submitted to the DJC for review. 

b. Herd management plan 

 The JCV, in conjunction with the herd owner, will develop a herd 

management plan to minimize the introduction and spread of MAP in 

the herd. A copy of the management plan must be submitted to the 

DJC for review and approval. 

Guidelines for developing a herd management plan are reviewed in the 

“Handbook for Veterinarians and Dairy Producers” third edition, 

2003; the “Handbook for Veterinarians and Beef Producers” third 

edition, 2003; and the “How to Do Risk Assessments and Management 

Plans for Johne’s Disease” 2003. Copies of these documents are 

available through the Ruminant Health Programs, NCAHP, VS. The 

herd management plan should review applicable topics outlined below 

under “3. Johne’s Disease Best Management Practices” that prevent 

the calves and young stock from becoming infected with MAP. 

 

3. Johne’s Disease Best Management Practices - General 
 17

a. Animal identification—All cattle should be individually identified 

using an identification method approved by the State animal health 

official. It is recommended that all animals in participating herds be 

individually identified using official eartags. Any regulations issued in 

9 CFR regarding animal identification with other animal health 

programs still apply. 

 

b. Minimum biosecurity measures—These measures are recommended to 

reduce exposure to manure or milk from cattle of unknown JD status. 

The herd management plan should emphasize the following 

biosecurity measures: 

1) Keep maternity and calving areas clean, dry, and free of 

manure. Wherever possible, use individual calving pens, or 

minimize cow density. The maternity and calving area should 

not house non-calving or sick animals, nor should it be 

immediately adjacent to mature animal housing areas. 

2) Ensure animals added to the herd come only from status-level 

or documented low-risk sources. Record the source and 

manage additions as higher risk animals unless you have 

evidence to the contrary. 

3) Minimize the exposure of young stock to manure from adult 

animals. 

4) Minimize exposure of livestock to other cattle and other 

susceptible animal species that may be infectious. 

5) Feed calves colostrum from an individual, identified, low-risk, 

test-negative cow, or a suitable quality colostrum replacer. 

6) Minimize contamination of feed, water, equipment, and 

vehicles with manure. 

7) Segregate, test, and remove clinical suspects from the herd as 

soon as possible. Make recommendations to reduce the risks 

from official test-positive cattle by humanely euthanizing the 

animals or sending them to slaughter. 

c. Best management practices—Dairy herd specific: 

 

1) Immediately separate from adult animals any heifer calves and 

bull calves that will be retained in the herd or sold for dairy 

purposes. 

2) After receiving colostrum, only give calves pasteurized milk or 

a quality milk replacer. 

3) Keep young stock free from exposure to the manure of mature 

cattle, house by age, and separate from older animals. 

d. Best management practices—Beef herd specific: 

1) Minimize the density of cow and calf pairs as much as 

possible. 
 18

2) Use feeding practices that reduce manure contamination of 

water, feed, and feeding areas as much as possible. 

3) Raise weaned replacement animals physically separate from 

older animals. 

4. Renewal 

To continue in the program, a herd owner and JCV must review and 

update the RAMP at least every 3 years after enrollment and make 

appropriate changes to the herd management plan. The updated RAMP 

must be submitted to the DJC between 60 days before and 60 days after 

the anniversary date. 

C. Herd Testing and Classification 

1. General 

Herd testing and classification constitutes the third level of participation in 

the program. The purpose of this component is to identify herds with a low 

prevalence of JD. 

2. Requirements for entry 

 

Herd owners enrolling in the herd testing and classification level must 

have a current approved RAMP in place, following the guidelines outlined 

in the management element (III.B.2). 

3. Testing 

Initial testing is required to determine the herd’s test status, using an 

appropriate testing strategy as listed in Appendix 2 under Level 1. 

Statistical subsets or greater numbers of cattle must be tested to establish a 

herd classification (see Appendix 1). 

All samples must be collected by, or under the supervision of, an 

accredited veterinarian, an animal health official, or authorized agent. All 

samples from herds whose owners are applying for herd classification 

must be submitted to an approved laboratory. 

a. Animals positive to a screening test should be classified as a suspect 

for MAP infection. It is recommended that the status of suspects is 

confirmed using an official JD test unless MAP has already been 

confirmed on the premises. Any animal classified as a suspect or 

infected should be officially identified. 

b. It is recommended that animals with positive results on an official JD 

test be identified as infected and restricted to the premises. When 
 19

infected cattle leave the herd, it is recommended that they be humanely 

euthanized or go directly to slaughter. 

Animals crossing State lines must do so in accordance with 9 CFR,

part 80, which requires an owner-shipper statement (a signed statement 

made by the owner or shipper) that declares the animal as infected; 

provides the official eartag number(s), origin, destination, consignor 

and consignee; and directs that the animal go directly to slaughter. 

c. The process for appealing the status of an official JD test-positive 

animal is described in Appendix 4. 

4. Herd classification 

 

a. Animal identification—All cattle must be individually identified using 

an official identification method approved by the State animal health 

official. Any regulations issued in 9 CFR regarding animal 

identification with other animal health programs still apply. 

b. Appealing a positive test—A test-positive animal’s status may be 

appealed using the appeal process described in Appendix 4. If an 

animal is removed from the herd while screening test results are 

pending, a fecal sample should be collected, submitted, and held at the 

laboratory. The DJC will make the final classification of the animal 

and herd. 

c. Herds enrolled in this component must use testing protocols approved 

by the DJC. Herd additions—At initial levels of the program, all 

purchased animals should be from herds with approved herd 

management plans. Heifers raised off the premises should be raised 

with at least the minimum biosecurity and control measures in place. 

At higher levels of the program, purchasing restrictions apply (see 

section III.C.5.c). 

5. Classification Testing 

a. The herd owners (with the JCV) should develop a testing protocol as 

follows: 

1) All animals specified in the testing protocol must be tested within 

10 to 14 months of the anniversary date. Multiple test dates are 

allowed including split-herd testing or rolling-herd testing 

provided that all animals are tested within the specific timeframe. 

2) Herds not adhering to the prescribed testing requirements will be 

placed in the management element. 

b. Testing 
 20

1) The classification system consists of levels 1 to 6 and is 

described in Appendix 2. Classification levels 1 to 3 identify 

herds with low test positive prevalence or an initial year of test 

negative results, and levels 4 to 6 identify herds with 2 or more 

years of test negative results. Levels 1 to 4 require annual 

testing. 

2) Vaccinated herds will be eligible for levels 4 to 6 after 

vaccination has been discontinued. Testing of vaccinated 

animals must be done using an official JD test; however, nonvaccinated herd mates may be tested using ELISA testing or a 

combination thereof. 

3) Herd removal provisions—If an animal in a classified herd tests 

positive to an official JD test in levels 4 to 6, or if the testing 

requirements are not followed, the herd must be downgraded to 

the appropriate classification level or removed from the 

classification element as determined by the DJC. 

c. Herd additions 

1) Purchased animals may be added to the herd, provided that: 

(a) For levels 1 to 3: 

 There are no purchasing restrictions at these levels of the 

program. However, it is strongly recommended that animals 

are purchased from sources with a classification level (or 

testing equivalent) that meets or exceeds that of the herd it is 

entering. 

(b) For levels 4 to 6: 

i. If purchasing animals from unclassified or levels 1 to 3 

herds, the herd will be demoted to level 3 (highest level 

of program without animal movement restrictions). 

ii. If purchasing animals from levels 4 to 6 herds: 

1. If the purchase is from the same or higher level 

than the herd’s classification, the herd retains its 

classification and no additional testing is 

required. 

2. If the purchase is from a lower level than the 

herd’s current classification, then: 

a. The herd will be dropped to the lowest 

level of the purchased animals. 
 21

OR 

b. The herd may maintain its current 

classification if all purchased animals 

from the lower status herd are tested 

three times with an OJT at 6-month 

intervals, starting at not less than 12 

months of age, and all tests are found to 

be negative. Purchased animals must 

then be included in the next herd 

classification test. 

(c) Once all herd additions have been granted status equal to 

the herd’s current classification, the herd may advance in 

the classification program by following the testing protocol. 

(d) Heifers raised off the premises must be raised with the 

proper biosecurity measures in place and with animals at an 

equal or greater classification level. 

(e) Classified herds may use embryos from other cattle herds if 

the embryos are processed according to International 

Embryo Transfer Society protocols. Embryo transfer 

recipient cows must meet herd addition requirements. 

(f) Purchasing a classified herd 

(i) If a classified herd is purchased, testing is not required 

if the purchased cattle remain on the premises. A new 

certificate will be issued in the new owner’s name. The 

anniversary date will remain the same. 

(ii) If part or all of a classified herd is purchased and the 

cattle move directly to a premises without cattle, they 

may retain their current classification level without 

testing; however, it is recommended that the risk of 

exposure to MAP from the environment is evaluated. A 

new certificate should be issued in the new owner’s 

name. The anniversary date of the new herd is 

established by the original classification date, unless a 

new herd classification test of the purchased cattle is 

requested. 

d. Herd level maintenance 

1) Herds at levels 1 to 3 must undergo a herd classification test 

annually to establish their classification level for the year. 
 22

2) Herds at levels 4 to 6 can maintain their classification by 

following any MAPDT strategy in Table 2 of Appendix 2. 

Testing for maintenance of herd classification must be repeated 

annually in level 4 herds; however, levels 5 and 6 herds are only 

required to test every 2 years from the classification date to 

maintain their herd classification. The level achievement year 

should be noted because continued monitoring increases 

confidence the herd is not infected. If a positive test is found 

during maintenance level testing in a level 4 to 6 herd, the herd 

will be reclassified to level 1of the program. Alternatively, the 

herd can elect to complete additional testing to attain a higher 

classification following the requirements for herd classification 

in Appendix 2. 

e. Renewal and advancement 

A herd will remain at any level for up to 14 months (up to 26 

months for levels 5 and 6 herds). For continuation of this 

classification, the herd owner must reapply with a copy of test 

results. An updated herd management plan (biosecurity plan) and 

an agreement to follow the classification component requirements 

must be submitted every 3 years. 

The herd owner can send the DJC a letter of intent to renew or 

advance if confirmation of screening test results will be received 

after the 14-month (or 26 month for levels 5 and 6 herds) deadline. 

If the letter of intent is received by 30 days after the deadline, the 

DJC may allow the herd to retain its status for up to 5 months. 

Herds for which the necessary test results have not been supplied 

by the extended 5-month deadline must be removed from the 

classification program. Herds removed from the classification 

program may retest and may be classified based on the results of 

testing used. 
 23

IV. Laboratory Procedures 

A. Approved Laboratories 

Official JD tests and screening tests used for the VBJDCP may be conducted 

in a private, university, State, or Federal laboratory. The State animal health 

official has the authority to decide if any laboratory passing the NVSL check 

test may participate in the State program. States should have the authority to 

periodically audit the JD diagnostic laboratories participating in the program. 

If a laboratory is outside of the State, the State may rely on audits conducted 

by the animal health officials from the State in which the laboratory is located. 

B. Laboratory Approval Process 

Check test proficiency panels must be passed annually in order for 

laboratories to be approved to participate in the VBJDCP for each testing 

format they plan to use. The check test procedures for participating in the 

annual proficiency tests are outlined below for MAPDT and ELISA tests. For 

further information, please contact NVSL’s Diagnostic Bacteriology 

Laboratory. 

1. Approval process for laboratories performing organism detection tests 

a. A laboratory seeking approval to perform MAPDT must contact 

NVSL for a proficiency test kit of 25 samples. A valid proficiency 

panel sample from NVSL will be determined by a consensus of at 

least 70 percent of the laboratories participating in the fecal culture 

check testing process. 

b. Laboratories must request a proficiency panel for each procedure or a 

standard operating procedure (SOP) that they wish to use for 

approved testing. Criteria for panel composition and grading may be 

obtained from NVSL and is also referenced in NVSL’s SOP-MB4011: Proficiency Panels for External Laboratory Assessment for 

Johne’s Disease Organism Based Tests. 

c. Laboratories requesting a pooled proficiency panel must also 

successfully complete and pass the corresponding individual panel 

using the same method. For example, laboratories requesting a pooled 

Herrold’s Egg Yolk (HEY) proficiency panel must also request and 

pass an individual proficiency test for HEY. 

d. The laboratory must not identify any of the negative test samples as 

positive samples. 

e. The laboratory must not identify any of the test samples classified as 

high levels of MAP (Too Numerous to Count or TNTC) as negative 

samples. 
 24

f. The laboratory must correctly identify at least 70 percent of the test 

samples that were not classified as negative or TNTC as positive 

samples. 

g. Laboratories performing culture may report a sample as 

“contaminated” and will be allowed sufficient time to reculture and 

report results without penalty. Contamination must be reported to 

NVSL first. Proficiency panel samples will contain at least 4 g of 

material to cover this possibility. 

h. The laboratory must use the same procedure and materials during the 

check test that are used during routine testing. If laboratory protocols 

are changed after certification is granted for the current year, a 

recertification test must be successfully completed, and a copy of the 

new protocols must be provided to NVSL. 

i. One retest per year is available if a laboratory fails the first time. Any 

laboratory that fails to pass the retake of the check test will become a 

nonapproved laboratory until the check test is administered again and 

passed the following year. 

2. Approval process for laboratories performing ELISA tests 

 

a. A laboratory seeking approval to perform ELISA testing must contact 

NVSL for a test kit of 25 samples. (A valid check sample will be 

determined by NVSL using available licensed ELISA kits.) 

b. Laboratories will report the ELISA score (sample to positive [S/P] 

ratio, ELISA score, and optical density values) of test samples and kit 

controls. 

c. Samples will be divided into extreme and intermediate samples based 

on consensus median values from all participating laboratories. 

d. Extreme samples (strong negative and strong positive) will be graded 

qualitatively. 

e. Laboratories that incorrectly identify any extreme test samples (graded 

qualitatively) will fail the proficiency test. 

1) Intermediate samples will be graded quantitatively using Z scores. 

Z scores indicate how many standard deviations away from the 

mean the score resides. A positive Z score indicates that the value 

is above the mean while a negative Z score indicates that the value 

is below the mean. 
 25

2) Laboratories must score within three Z scores of the mean value to 

correctly identify a serology proficiency test sample. 

3) Laboratories with more than two quantitative (Z scored) test results 

outside the acceptable range will not pass the proficiency test. 

4) A Z score calculation will be used to determine variation of 

quantitative results. A major advantage of the Z score grading 

system is that it allows laboratory feedback on whether 

laboratories are consistently above or below the consensus median 

value. Calculating absolute values allows a visual representation of 

consistency, since a laboratory that is not consistently above or 

below the median will still have a large absolute value Z. 

5) Laboratories with an absolute average Z score of greater than two 

will be notified that quality control practices should be evaluated. 

Specific actions could include requiring internal quality control 

review using NVSL’s low positive sera, contacting the kit 

manufacturer, and evaluating other equipment and procedures. 

6) The laboratory must use the same procedure and materials during 

the proficiency test that are used during routine testing. 

7) One retest per year is available if a laboratory fails the first time. 

Any laboratory that fails to pass the retake of the check test will 

become a nonapproved laboratory until the check test is 

administered again and passed the following year. 

3. Continuing quality assurance 

Producers and veterinarians must have confidence in the quality of 

serology results they receive. To ensure the credibility of the infection 

status assigned as a result of testing under the guidelines of the national 

control program, each approved laboratory should run low positive quality 

control sera purchased from NVSL to monitor variations in testing results. 

NVSL will provide the current protocol for running and submitting the 

data from the quality controls. 

4. Reporting 

 To monitor VBJDCP activity, testing conducted at approved laboratories 

must be reported to the State animal health official. Data from the 

laboratory must be reported monthly or as required by the State animal 

health official. Data should be reported and sorted by the State in which 

the herd resides. The minimum required data for national reporting 

includes: 
 26

a. Number of herds tested by screening tests, sorted by method of 

detection and species 

b. Number of screening test positive results, sorted by method of 

detection and species 

c. Number of herds with test-positive results by screening tests, sorted by 

method detection and species 

d. Number of official JD tests submitted and run, sorted by method of 

detection and species 

e. Number of herds tested by official JD tests, sorted by method of 

detection and species 

f. Number of official JD test results that are positive for MAP, sorted by 

method of detection and species 

g. Number of herds with positive results by official JD test, sorted by 

method of detection and species 

5. If the required data are not reported on a timely basis, the State animal 

health official may refuse to allow a laboratory to do State program testing. 

It is recommended that the State animal health official require that all JD 

test results be reported to the State. 

C. Approved Program Tests 

1. Official Johne’s disease test (OJT)—An organism detection test done on 

an individual sample from a single animal approved by the Administrator 

and conducted in a laboratory approved by the Administrator. 

a. Fecal and tissue culture—Culture is the standard for organism-based 

tests. Methods include both solid and liquid culture preparations. 

Protocols for recommended methods can be obtained from NVSL 

upon request. Fecal and tissue cultures are considered an MAPDT. 

b. Direct fecal polymerase chain reaction (PCR)—Direct PCR tests can 

detect the presence of MAP without having to grow it. An advantage 

of the PCR test is that it takes less than 3 days to conduct. However, 

the disadvantages are higher cost and the potential of missing low 

shedders. Direct fecal PCR tests are considered an MAPDT. 

c. Histology of tissue—A check test is not available at this time. 

Microscopic identification of the characteristic pathological changes 

and of MAP organisms in tissue is a definitive test for JD. Tissue 

changes and bacteria can be observed in the intestinal lining and in 

nearby ileal, mesenteric, and ileocecal lymph nodes in infected 
 27

animals. Sensitivity depends on the stage of disease, the number and 

type of specimens collected, and the experience and time spent 

examining tissues by the pathologist. 

2. Screening test—Tests that do not meet the 9 CFR 80 definition of an 

official JD test but are used for herd classification. Screening tests are 

tools that have been developed to aid in determining the presence or 

absence of MAP within a herd. Depending on the method, screening tests 

may include individual animals or multiple animals in a diagnostic 

sample. 

a. USDA approved ELISA—Animals found positive by ELISA tests 

should be considered suspect until confirmed using an OJT for lowlevel risk herds. ELISA tests are to be used as screening tools or to 

help make management decisions. 

b. Environmental fecal sampling—Fecal material samples collected in 

areas where a large proportion of the herd is commingled. Samples 

are tested using organism detection methods in approved 

laboratories. The sampling protocol is available in Appendix 2. 

c. Pooled fecal cultures or PCR—Fecal samples collected from 

individual animals that are pooled together in groups of five. 

Individual samples should be submitted to laboratories approved for 

fecal pooling and tested by an organism detection test. The pooling 

protocol is available in Appendix 2. Pooled fecal cultures or pooled 

fecal PCR tests are considered an MAPDT. 
 28

Appendix 1: Sampling Sizes and Random Selection for Statistical Subset 

Testing 

Sample Sizes 

Table 1. Sampling sizes for statistical subset testing 

Number of cattle in herd 

(36 months or older) 

Minimum Number of Cattle to Sample 

(36 months or older) 

ELISA Testing MAP Detection Test 

≤ 300 Test all Test all 

301 – 400 Test all Test all (up to 313) 

401 – 500 Test all 324 

501 – 600 Test all (up to 531) 332 

601 – 700 540 338

701 – 800 547 342

801 – 900 552 345 

> 901 580 360 

In smaller herds, all cattle 36 months of age and older must be tested. In herds 

with fewer than 30 animals that are 36 months of age or older, animals 24 months 

of age or older must also be tested. 

The sample numbers above are based on the following assumptions: 

 

 The cattle to be tested are 36 months of age or older. 

 ELISA tests are assumed to have 25 percent sensitivity, and fecal cultures 

are assumed to have 40 percent sensitivity. These were consensus 

estimates of the Herd Status Committee of the National Johne’s Working 

Group of the United States Animal Health Association Committee on 

Johne’s Disease in 1998 for cows 24 months of age or older with 

subclinical infections. No changes were made for older populations 

sampled. 

 ELISA and fecal culture are assumed to have 100 percent test specificity 

(given followup of all ELISA positives with fecal culture). 

 The calculations are based on sampling without replacement. 

Random Selection Procedures or Statistical Subsets 

The authorized agent should randomly select and sample the appropriate 

number of eligible cows. This works in small herds or in herds where the 

animals can be easily caught. For a more scientific method, select animals 

using a random number generator or random number tables. 
 29

If the list is made in random order, a systematic sampling can be used on the 

list (i.e., selecting every nth individual from a list [or coming through a chute] 

after choosing a random number from 1 to n as a starting point). Determine n

by dividing the number in the herd by the required sample size needed in the 

statistical subsets). 

Large herds should use a stratified randomization approach to collect a more 

representative sample. The number of animals in each group should be 

determined (e.g., high producers, low producers, and dry cows) and the 

percentage of each type of animal computed. The percentage of samples 

collected from each group should equal the percentage of each group of 

animals in the herd (i.e., if 10 percent of the animals in the herd are low 

producers, then 10 percent of the samples should be collected from low 

producers). Sampling in each group would be done by simple or systematic 

sampling. 

These will not be perfect randomized sample collections, but they are better 

than convenience sampling. Unless the producer is suspicious of infection in 

the herd, targeting ‘high-risk’ animals is not the method to use. Testing highrisk groups or target testing should be reserved for herds in the management 

or control programs. All testing for herd classification should be as close to 

random as possible. 
 30

Appendix 2: Approved Testing Strategies for the Classification Component

The program levels are established to provide herds with a lower risk of 

transmitting MAP, a way to demonstrate years of participation and progress in the 

program. An alternate testing strategy may be approved for any level as long as it 

meets or exceeds the testing sensitivity for the given testing level as approved by 

the DJC. 

The classification system was developed based on review of scientific literature, 

data analysis, and discussions by a team of experts in the fields of epidemiology, 

diagnostics, and cattle management systems. 

I. Concepts applied in development of JD Herd Test Strategies 

A. Unknown status. Untested herds or herds not desiring classification will 

not be given a JD classification level. 

B. Eligible cattle. Test-eligible cattle for testing will include all cattle 36 

months of age and older and male bovine animals 24 months of age or 

older. Subset sampling will be based on Appendix 1, with a maximum of 

580 cattle randomly sampled for ELISA and 360 for MAPDT. Herds will 

be categorized by herd size based on the number of eligible adult cattle 

3 years of age or older. 

C. Eligible tests. All ELISAs that have passed the NVSL check test will be 

considered as equivalent for herd categorization. All official Johne’s 

disease tests (OJT) (individual MAPDT) that have passed the NVSL check 

test will be considered as equivalent for herd categorization. The option is 

available for followup testing of ELISA positive cattle with an OJT. For 

pooled fecal testing using MAPDT, the required cattle sample will be 

collected individually and tested in groups of five cattle per pool by the 

laboratory. Herd classification categories are based on statistical 

probabilities (the upper 95 percent confidence limit for within-herd 

prevalence is below the specified values for classification levels 1 to 6) 

with minor adjustments made for practicality of on-farm sampling and 

internal consistency. 

D. Herd classification based on test results. Cattle herds in the initial year of 

testing will be placed in classification levels 1 to 3 with whole-herd test of 

test-eligible animals or subset testing for large herds as described in 

Appendix 1, Table 1, or in level 1 with a minimum sampling herd test 

(Appendix 2, Table 2). After the second year of testing with no positive 

test results, cattle herds can be upgraded into level 4; after the third year, 

into level 5; and after the fourth year, into level 6. Categorization of herds 

should be made using critical threshold levels (Appendix 2, Table 1) 

without rounding. Herds can be placed in levels 1 to 3 with positive test 

results after herd testing. Herds with positive test results are not allowed in 

levels 4 to 6. For herds using pooled MAPDT, the option exists to test 

individual cows from positive pools and calculate the percentage of 

MAPDT-positive cows to assign an appropriate classification level using 

the individual MAPDT line from Table 1 (Appendix 2). Any positive pool 
 31

that subsequently yields all negative individual MAPDT results will be 

considered as one positive individual MAPDT. 

E. Adjustment to Classification Levels. The designated Johne’s coordinator 

can make adjustments to the herd classification level based on available 

data and best judgment. 

II. Example Situations 

A. A dairy herd with 150 cows (n=100 cows 36 months of age or older) 

without previous status in the existing Test Negative Program could 

choose to test all eligible cattle (n=100) using ELISA (and could choose 

ELISA/MAPDT option if desired), individual MAPDT, or pooled 

MAPDT. If ELISA is chosen as a test option, one positive ELISA would 

result in classification level 2 (≤1.5 percent in the 100-199 cattle 

category). If individual MAPDT is chosen, three positive OJT would 

result in classification level 2. The herd owner could choose to test a 

minimum number of randomly selected cattle (60 for ELISA or 30 for 

individual MAPDT) tested using ELISA or MAPDT, or use environment 

fecal MAPDT to achieve level 1, assuming no positive results are 

obtained. 

B. A beef herd with 80 cattle 36 months or older and already at level 2 of the 

current Test Negative Program desires to advance within the program. The 

herd will be placed at classification level 3 with a pooled MAPDT or 

could move to level 4 by testing all eligible cattle with individual 

MAPDT, if all tests are negative. 

C. If the herd size is between 1and 99, individual MAPDT must be used to 

advance to level 4. The following year pooled MAPDT may be used to 

advance. In the case where the herd size is between 100 and 199, 

individual ELISA samples or individual MAPDT must be used to advance 

to level 4. The following year pooled MAPDT may be used to advance. 
 32

Table 1. Herd Testing Strategies to Achieve JD Herd Classification Levels 

*ELISA/Ind MAPDT—ELISA with followup individual MAPDT 

▲Environment MAPDT—This testing strategy is only available for dairy herds 

(not beef herds) 

■

Herd size—Number of the test-eligible animals in the herd

Herd 

Size■ Testing Strategy 

Herd Classification level 

1 2 3 4 5 6 

Maximum proportion positive to achieve level (no 

rounding) 

1 - 99 

ELISA ≤1.5% 0% 

ELISA/Ind MAPDT* 0% 

Individual MAPDT ≤6% ≤2% 0% 0% 0% 0% 

Pooled MAPDT ≤15% 0% 0% 0% 0% 

Environment MAPDT▲ 0% 

100 - 199 

ELISA ≤2.5% ≤1.5% ≤0.5% 0% 0% 0% 

ELISA/Ind MAPDT ≤1.0% 0% 

Individual MAPDT ≤6.5% ≤3.5% ≤1.5% 0% 0% 0% 

Pooled MAPDT ≤15% ≤10% 0% 0% 0% 

Environment MAPDT 0% 

200 - 299 

ELISA ≤3.5% ≤2% ≤1% 0% 0% 0% 

ELISA/Ind MAPDT ≤1.5% ≤0.5% 0 % 

Individual MAPDT ≤7% ≤4% ≤1.5% 0% 0% 0% 

Pooled MAPDT ≤13% ≤10% ≤6% 0% 0% 0% 

Environment MAPDT 0% 

≥ 300

ELISA ≤4.0% ≤2.5% ≤1% 0% 0% 0% 

ELISA/Ind MAPDT ≤2.0% ≤1% ≤0.5% 0% 0% 0% 

Individual MAPDT ≤7.5% ≤5.0% ≤2% 0% 0% 0% 

Pooled MAPDT ≤11% ≤7% ≤5% 0% 0% 0% 

Environment MAPDT 0% 
 33

Table 2. Minimum herd testing options for entry into program at 

classification level 1 or maintenance of classification levels 4 through 6, if no 

positive test results are obtained 

Test Minimum number cattle to test* 

ELISA 60 

ELISA/Ind MAPDT 60 

Individual MAPDT 30 

Pooled MAPDT 6 pools (30 cattle) 

Environment MAPDT 6 environmental fecal samples 

* If the test-eligible herd has fewer animals than the minimum number to test, refer to 

Appendix 2, Table 1, for testing options based upon test-eligible herd size. If there are 

any positive test results from the minimum herd test, producers may elect to test the 

remainder of animals needed to classify the herd according to Table 1. 

III. Collection and Processing Protocols 

A. Environmental Fecal Sampling (For dairy herds only) 

From each dairy farm, collect two composite environmental fecal samples 

tested by an MAPDT from each of the following locations on the farm: 

manure concentration areas (cow housing alleyways or gutters), manure 

storage areas (lagoons, piles, pits, or manure spreader), and another 

manure concentration area (sick cow pens or other cow alleyways and 

travel-ways). A total of six samples should be collected for submission to 

the diagnostic laboratory. 

Each composite environmental fecal sample should contain approximately 

20 g of fecal material with bedding or soil from a minimum of four 

different sites within each sampling location. Collect each sample with a 

separate disposable latex glove, place in a 95-mL plastic-covered 

specimen container labeled with the sampling location and herd identifier, 

and store in a cooler with ice during transport to the laboratory. Be sure to 

include sufficient manure in the sample when sampling from well-bedded 

areas such as sick cow pens or loose-housing lots. 

In free stall barns, obtain each cow alleyway sample from a minimum of 

four sites across cow alleyways, collected to represent most of the mature 

cows (24–36 months of age and older) within the farm. Crossovers (areas 

around waterers, corners, and ends of scrape lanes) are excellent places to 

collect well-mingled manure subsamples. 

In tie stall barns, obtain samples from all gutters containing manure from 

mature cows (24 months of age and older). Other suitable locations for 

subsampling are places where the gutter cleaner exits the barn, along the 

ramp, and in corners. 
 34

Sample manure storage lagoons (using personal precautions for safety) 

from four locations at the perimeter of the lagoon by submerging the 

sampling container up to 10 cm beneath the water’s surface. 

Each composite sample from manure piles should be obtained from four 

different sites up to 10 cm beneath the surface. 

Each composite sample from manure pits can be collected using two to 

three sterile 4 × 4 gauze pads tied to fishing line with fishing weight and 

soaked at least 10 cm below the manure’s surface. 

(Modified from Raizman, et al., 2004) 

B. Random Pooled MAPDT 

Submit individual fecal samples of 30 randomly selected test-eligible 

animals to be tested by an MAPDT in 6 pools of 5 animals each. Submit 

individual samples to laboratories approved for fecal pooling. 

Herds with fewer than 30 test-eligible animals can still use fecal pooling. 

All animals 24 months or older are to be included until a total of 30 

animals has been reached or all 24-month-old animals have been tested. At 

least 3 pools of 5 (15 animals) should be available to use pooling. If 15 

animals are not available, individual samples should be used. 

Fecal Pooling Procedure 

1. Fecal pooling procedure – to be done in the laboratory – five samples 

per pool 

a. Homogenization by stirring 

Weigh out 2 g of each sample to be pooled and place into a sterile 

50 ml conical centrifuge tube. Mix samples by stirring with a 

sterile wooden stick. Vortex samples vigorously for 10 to 15 

seconds until the mixture appears homogeneous. Remove 2 g of 

the resulting mixture for processing and testing by routine method 

used in laboratory. 

b. Homogenization by stomaching 

Weigh out 2 g of each sample to be pooled and place into a 

stomacher bag. Be sure to add the samples to the same corner of 

the bag to ensure even mixing. Stomach the samples on the highest 

setting for 2 minutes. Inspect the mixture to determine if it appears 

homogeneous. Additional stomaching may be required to 
 35

homogenize the mixture. Remove 2 g of the resulting mixture for 

processing and testing by routine method used in laboratory. 

IV. References 

1. Collins M. T., Gardner I. A., Garry F. B., Roussel A. J., Wells S. J., 2006. 

Consensus recommendations on diagnostic testing for the detection of 

paratuberculosis in cattle in the United States. J Am Vet Med Assoc.

229(12):1912-9. 

2. Raizman, E. A., Wells, S. J., Godden, S. M., Bey, R. F., Oakes, M. J., 

Bentley, D. C., and Olsen, K. E., The Distribution of Mycobacterium 

avium ssp. paratuberculosis in the Environment Surrounding Minnesota 

Dairy Farms, J. Dairy Science 87:2959-2966, 2004. 

3. Tavornpanich S., Muñoz-Zanzi, C.A., Wells, S.J., Raizman E.A., 

Carpenter T.E., Johnson, W.O., Gardner I. A. 2007. Simulation model for 

evaluation of testing strategies for detection of paratuberculosis in 

Midwestern US dairy herds. Prev Vet Med. Aug 22; [Epub ahead of print]. 

4. Van Schaik, G. et al. 2003. Pooled fecal culture sampling for 

Mycobacterium avium subsp. paratuberculosis at different herd sizes and 

prevalence. J Vet Diagn Invest 15:233-241. 

5. Wells, S.J. et al. 2003. Evaluation of bacteriologic culture of individual 

and pooled fecal samples for detection of Mycobacterium 

paratuberculosis in dairy cattle herds. JAVMA 223:1022-1025. 

6. Wells, S. J. et al. 2002. Evaluation of bacteriologic culture of pooled fecal 

samples for detection of Mycobacterium paratuberculosis. A JVR

63:1207-1211.
 36

Appendix 3: Johne’s Disease Certified Veterinarian Training Guidelines 

 

I. Initial Certification Training 

A. Johne’s Disease Overview 

1. Description (strains and survival) 

2. Pathogenesis (host susceptibility, stages of disease, differential 

diagnosis) 

3. Transmission pathways (fecal/oral, colostrum/milk, prepartum, saliva, 

artificial insemination, embryo transfer [E.T.]) 

4. Pass-through events 

B. Disease Prevention Management 

1. Directed at enhancing biosecurity 

2. Include general principles and point out differences between dairy and 

beef herd management practices 

3. Prevent entrance of MAP

4. Risk from herd additions and replacements (include E.T. recipients 

and herd bulls) 

5. Risk from environment (vehicles, water, feed, etc.) 

 

C. Disease Control Management 

1. Directed at reducing risk for pathogens 

2. Include general principles and point out differences between dairy and 

beef herd management practices to break the infection cycle, prevent 

ingestion, prevent spread, and decrease pathogen load in the 

environment 

3. Cover manure management in specific animal environments such as 

newborns, suckling and weaned calves, yearling and bred heifers, and 

mature animals 

4. Provide information on colostrum and milk management with 

emphasis on pooled versus individual feeding, effect of feeding 

unpasteurized hospital or waste milk, and methods of onsite 

pasteurization 
 37

5. Include strategies for managing infected animals through animal 

identification, removal/separation management, and provide 

information on the importance of protecting susceptible young stock 

and reducing the environmental pathogen load 

6. Provide ideas for the management of replacements and/or additions 

including biosecurity of heifers raised off-site, knowing the risk of the 

source herd of additions and strategies to buy from low-risk sources 

7. Develop a risk management plan based on assessment 

D. Overview of Diagnostic Tests 

1. Types of tests being used 

a. ELISA 

b. Fecal culture 

c. Agar gel immunodiffusion 

d. PCR 

e. Biopsy 

f. Gamma interferon 

2. Interpretation of test results 

a. Sensitivity and specificity 

b. Likelihood ratio 

c. Predictive values 

d. Interpretation at the herd level 

e. Interpretation at the individual animal level 

3. Discuss differences in strategies for testing to determine herd 

prevalence, enhancing control, measure herd progress, purchasing herd 

additions, and participating in the VBJDCP 

E. Overview of RAMPs 

1. The information in the handbooks is the cornerstone for conducting 

risk assessments and developing management plans (“Handbook for 

Veterinarians and Dairy Producers” and “Handbook for Veterinarians 

and Beef Producers”). 

2. Each book should be covered in enough detail to ensure that 

veterinarians are able to collect required data, perform risk 

assessments, and complete management plans with their clients. 

3. The instructional handbook, “How to Do Risk Assessments and 

Management Plans for Johne’s Disease” is recommended as a guide 

for specific information details. 

 
 38

F. Overview of Uniform Program Standards for the Voluntary Bovine 

Johne’s Disease Program 

1. Responsibilities of the JCV in the JD program 

2. Explanation of the requirements for the management element and herd 

testing and classification element on the VBJDCP 

 

G. Overview of Specific State Regulations and Program Standards

H. Model Time Allotments for the Actual Training Sessions (6 to 8 hours) 

1. Topics to be included: 

a. Overview of JD pathology and epidemiology in cattle (1 hour) 

b. Management strategies for preventing JD in dairy and beef herds 

(30 minutes) 

c. Management strategies for controlling JD in dairy and beef herds 

(30 minutes to 1 hour) 

d. Overview of diagnostic tests (1 to 2 hours) 

(1) Types and interpretation of results including predictive values 

e. Strategies for use (30 minutes) 

2. How to use handbooks (2 hours) 

a. Information collection 

b. Risk assessment 

c. History, prevalence, and management practices 

d. Testing strategy 

e. Management plan development – Link back JD management to 

existing management and owner goals 

3. Uniform Program Standards for the Voluntary Bovine Johne’s Disease 

Program (30 minutes to 1 hour) 

4. State specific regulations and program standards (30 minutes) 

II. Recertification Training 

A. Required Topics 

1. Review of JD basics 

2 Epidemiology update 

3. Testing and interpretation 

a. New and emerging tests 

b. Best tests for different scenarios 

4. National and State program review, highlighting any changes 
 39

5. JD economics and marketing tips 

B. Additional Suggested Special Challenges and Topics 

1. Correcting common misconceptions (identified by DJC) – Case 

scenarios 

2. Update on research regarding the zoonotic issue 

3. Vaccine usage 

4. Potential use of JD “control” products 
 40

Appendix 4: Appealing the Status of a Test-positive Animal 

I. For animals found positive to a screening test, a herd owner may elect to 

confirm the test results as follows: 

A. An official JD test must be submitted by an accredited veterinarian within 

45 days of notification of the screening test results. 

B. The herd will be classified based upon the initial test results. If the status 

of a positive animal is appealed, the herd classification may be changed 

based upon the discretion of the DJC and the guidelines in Table 1 of 

Appendix 2. The animal must be included in the next round of program 

testing if it remains in the herd. 

C. If the animal that was test positive to a screening test has left the herd so 

that no confirmation of the results can be obtained, the herd maintains its 

classification based upon the original herd test. 

II. To appeal positive results to an official JD test, a herd owner must submit a 

written statement to the DJC within 30 days of the positive results to request 

an appeal, and then, at his or her own expense, arrange for an accredited 

veterinarian to: 

A. Conduct a necropsy of the animal with an official JD test on tissue and 

histopathology of the ileum and of the mesenteric and ileocecal lymph 

nodes; or 

B. Conduct a full-thickness biopsy of the ileum and biopsy of the mesenteric 

or ileocecal lymph nodes with histopathology and an official JD test on 

tissues and fecal samples taken at the time of biopsy; or 

C. Submit six separate, serial fecal samples from the animal, with samples 

collected between 30 and 45 days apart for an official JD test. All six 

samples must be negative for the animal to be considered a test-negative 

animal. 

D. The herd JD status will be suspended until all testing is completed. The 

herd will be classified at the DJCs discretion, based upon the test results 

and the appropriate classification in Table 1 of Appendix 2.